Examples with KAlignerParameters com.milaboratory.core.alignment.kaligner1.KAlignerParameters used on opensource projects

Example 6 with KAlignerParameters

use of com.milaboratory.core.alignment.kaligner1.KAlignerParameters in project mixcr by milaboratory.

the class VDJCAlignerParametersTest method test1.

@Test
public void test1() throws Exception {
    VDJCAlignerParameters paramentrs = new VDJCAlignerParameters(new KGeneAlignmentParameters(GeneFeature.VRegion, 120, 0.87f, new KAlignerParameters(5, false, false, 1.5f, 0.75f, 1.0f, -0.1f, -0.3f, 4, 10, 15, 2, -10, 40.0f, 0.87f, 7, LinearGapAlignmentScoring.getNucleotideBLASTScoring())), new DAlignerParameters(GeneFeature.DRegion, 0.85f, 30.0f, 3, AffineGapAlignmentScoring.getNucleotideBLASTScoring()), new KGeneAlignmentParameters(GeneFeature.JRegion, 120, 0.87f, new KAlignerParameters(5, false, false, 1.5f, 0.75f, 1.0f, -0.1f, -0.3f, 4, 10, 15, 2, -10, 40.0f, 0.87f, 7, LinearGapAlignmentScoring.getNucleotideBLASTScoring())), new KGeneAlignmentParameters(GeneFeature.CExon1, 120, 0.87f, new KAlignerParameters(5, false, false, 1.5f, 0.75f, 1.0f, -0.1f, -0.3f, 4, 10, 15, 2, -10, 40.0f, 0.87f, 7, LinearGapAlignmentScoring.getNucleotideBLASTScoring())), VJAlignmentOrder.JThenV, false, false, 120.0f, 5, 0.7f, false, false, false, PairedEndReadsLayout.Opposite, new MergerParameters(QualityMergingAlgorithm.SumSubtraction, null, 12, null, 0.12, Unweighted), false, 5, 120, 10, true);
    String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs);
    VDJCAlignerParameters deser = GlobalObjectMappers.PRETTY.readValue(str, VDJCAlignerParameters.class);
    assertEquals(paramentrs, deser);
    VDJCAlignerParameters clone = deser.clone();
    assertEquals(paramentrs, clone);
}